BBE Newsletter Fall 2023

Beckman Institute News

PILOT PROJECTS AND SINGLE CELL LAB

Three new Beckman Institute Pilot Projects have been approved for the 2023-24 academic year, each offering cutting-edge resources to interdisciplinary researchers at Caltech. In addition, the Cell Interaction Initiative, an integration of multiple resource centers, is expected to open in Fall 2023.

Pilot Projects Explore New Avenues

The BI Pilot Program offers support for innovative and exploratory initiatives, many of which have gone on to become fully developed resource centers or facilities. Applications are solicited annually in March, and successful proposals receive up to three years of funding (up to $125,000 per year). The 2023 Pilot Project cohort supports new directions in biological imaging, genetic sequencing, and analytics.

The Center for Deep-Tissue Molecular & Cellular Imaging and Control (DeepMIC) applies imaging tools that are common in medical applications – such as MRI and ultrasound – to basic biomedical research, where they are less readily available but can provide powerful insights. Under the direction of Professor Mikhail Shapiro and Dr. Di Wu, DeepMIC is also developing new tools for imaging and analysis; its staff will assist researchers from across campus in everything from training on existing and new tools to experimental design. In collaboration with established BI Centers, including CLOVER, SPEC, and the Neurotechnology Lab, DeepMIC will leverage new applications of deep-tissue imaging tools to help researchers better understand basic biological functions within their anatomical context.

Focusing on interpreting rather than creating images, the Center for Image Analysis (CIMA) will provide automated approaches to processing and analyzing images produced by various microscope modalities. CIMA provides tools to automate and streamline some of the processes involved in annotating and interpreting images produced by other Beckman Institute resource centers, such as the Cryo-EM Center and the Bioimaging Facility. Directed by Dr. Alexandre Cunha and Professors David Glover, Elliot Meyerowitz, Ellen Rothenberg, and Magdalena Zernicka-Goetz, CIMA aims to empower researchers to spend less time processing images and more time focusing on the science.

The third pilot project, directed by Dr. Anna Romano and Professor Rustem Ismagilov, aims to make emerging approaches for quantitative, low-biomass microbial sequencing available to the Caltech community. The importance of microbial study in contexts from the environment to the human gut is well established, but sequencing and analyzing genomic data from samples with low microbial biomass remains a challenge. This pilot project offers a pipeline of integrated, streamlined technologies to conduct quantitative sequencing of bacteria, archaea, and fungi; remove human DNA from samples through the microbial enrichment method (MEM); and provide computational tools for data analysis, experimental design, and data interpretation. If successful, the pilot project will lay the groundwork for a future Quantitative Microbiome Resource Center (QMRC) to expand the scope and impact of this work.

Cell Interaction Initiative Launches

The Cell Interaction Initiative (CI2), to be housed in Beckman Institute 227, is the culmination of a years-long effort to enable single cell researchers to access many of Caltech’s complementary resources and facilities at a single shared location.

CI2 features the Berkeley Lights Beacon instrument, which utilizes optofluidics (the ability to physically manipulate cells with light) to isolate, culture, and characterize cells within microfluidic chips. The Beacon can be used to culture cells for days or weeks at a time; it is a powerful, high-throughput system that has the capacity to screen tens of thousands of cells at once, and, crucially, allows for observation of isolated single cells in addition to overall patterns. This technology also makes it possible to recover single cells from microfluidic chips. The Beacon Center, under the direction of Professor Pamela Bjorkman and Dr. Kate Malecek, was launched as a BI Pilot Program in 2022. CI2 combines the power of the Beacon instrument with other campus resources devoted to single cell research. Sequencing of cells, among other capabilities, is conducted by another BI resource center, the Single Cell Profiling and Engineering Center (SPEC, PI: Professor Matthew Thomson, Director: Dr. Brian Williams). And Dr. Jost Vielmetter (Director, Protein Expression Center), another core member of the CI2 group, will be providing advanced automated methods for conducting protein screens and validating properties of individual cells and proteins through automated protein library production, biochemical and cell-based assays, and more.

A major donation to the Beckman Institute by Dr. Martin Nemko will enable the renovation of room 227 to accommodate both the Beacon instrument and its complementary resource centers. Housing these separate approaches to single cell research within a shared space enables researchers to seamlessly move from one type of analysis to another, thus advancing both the mission of each individual resource center and the state of the art of single cell research at Caltech. Malecek, Williams, and Vielmetter, as the three lead scientists affiliated with the new Initiative, are excited to share these resources with the campus community. If you are interested in learning more about how the Beacon instrument or CI2 resources can contribute to your research, contact Kate Malecek at kmalecek@caltech.edu to schedule a consultation.

Written by Ariane Helou, Scientific Writing Specialist, Beckman Institute

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Betty Hong Receives Tenure!

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Betty Hong was promoted to the rank of Professor on July 1st! Faculty, family and friends celebrated at The Old Mill in San Marino on August 17th. Congratulations Betty!

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Welcome Assistant Professor Zhen Chen

Please welcome Assistant Professor Zhen Chen who joined BBE on October 1st!

Zhen aims to develop cryo-electron tomography to understand macromolecular machines and solve biological questions. He believes Caltech is an excellent place to study cilia biology, his current research direction, as well as other biological systems that play important roles in biomedical, environmental and energy research. Ultimately, he would love to build or reconstitute the molecular machines to test if we truly understand the fundamental mechanisms of the system.

Outside the lab, Zhen enjoys sharpening his imaging techniques by taking photos of the starry sky and beautiful landscapes during sunrise or sunset. These activities often draw him into the middle of nowhere at times that are either too early or too late.

Zhen's lab is located on the third floor of Broad. Stop by his office in room 359 to introduce yourself!

Dianne Newman Receives 2023 AGU Honor

Each year, AGU (American Geophysical Union) recognizes individuals and teams for their accomplishments in research, education, science communication and outreach. Honorees and their scientific efforts have transformed our understanding of the world, impacted our everyday lives, improved our communities and contributed to solutions for a sustainable future.

Dianne Newman was elected as a 2023 AGU Fellow for her discoveries of molecular mechanisms that allow us to track and interpret biogeochemical signatures in both modern and ancient environments. Congratulations Dianne!

David Baltimore Chair in Biomedical Research Established

On September 22, the Whitehead Institute honored Nobel Laureate David Baltimore by establishing the David Baltimore Chair in Biomedical Research. Baltimore is the founding director of the Whitehead Institute for Biomedical Research. Watch the presentation.

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Victoria Orphan Recognized as the LGBTQ+ Scientist of the Year

Victoria Orphan received the LGBTQ+ Scientist of the Year honor in June for her outstanding contributions to science and her commitment to diversity, equity, and inclusion. The award was granted by Out to Innovate, a global organization of LGBTQ+ (lesbian, gay, bisexual, transgender, queer) students and professionals in STEM, which also honors an LGBTQ+ educator and engineer each year. Victoria and other awardees were honored on September 9th in a virtual ceremony with a keynote address by Nobel Laureate Carolyn Bertozzi.

Michael Roukes Wins NIH Director's Transformative Research Award

Michael Roukes has been awarded the National Institute of Health's (NIH) Director's Transformative Research Award!

This award, granted to only six scientists nationwide this year, "supports individuals or teams proposing transformative projects that are inherently risky and untested but have the potential to create or overturn fundamental paradigms," according to the NIH.

Faculty Archives

Barbara McClintock

Perhaps the century’s most famous maize geneticist, Barbara McClintock, had initiated cytological studies of maize chromosomes in Rollins Emerson’s Plant Breeding Department at Cornell. Having thoroughly defined the connection between linkage groups and the ten maize chromosomes, McClintock came to Caltech as a research fellow between 1931-33 when she worked with Ernest Anderson. After spending some time in Germany as political tensions were rising in the early 1930s, she moved to the University of Missouri before finally accepting a Position in the Carnegie Institute’s Genetics Laboratory at Cold Spring Harbor. Here she would carry out her groundbreaking work using classical genetic approaches to demonstrate the existence of mobile genetic elements in maize, for which she won the Nobel Prize in 1983. During her time at Cold Spring Harbor, she would join Caltech as a visiting professor in 1946 and in 1954.

This is an excerpt from the full genetics display to be unveiled in Parsons-Gates second floor in early 2024. Written by David Zierler and Prof. David Glover.

10 years of BBE

This year marks a decade since the Division of Biology voted to incorporate the growing discipline of bioengineering and to change its name to the Division of Biology and Biological Engineering (BBE).

As a result of this reorganization, the number of faculty members in the division grew considerably, with 10 joint appointments awarded to researchers in other divisions whose work had a bioengineering focus. “Modern research in biology is increasingly intertwined with technological advances,” says Richard Murray, the William K. Bowes Jr. Leadership Chair of the Division of Biology and Biological Engineering. “Those technological advances in turn allow the possibility of providing new solutions to societal problems, ranging from human health, to sustainability, to new materials and devices.”

The transformation combined the division’s traditional academic concentrations—genetics, biochemistry, developmental biology, immunobiology, microbiology, molecular biology, and neurobiology—with its newly established strengths in the fields of bioengineering, genomics, synthetic biology, and computational biology.

Written by Lori Dajose

WiBBE Welcome Back Happy Hour, October 12, 4pm, Broad Cafe Patio

Special Biochemistry Seminar, October 13, 2-3pm, Crellin 151

BioRender 101 Training (please register), October, 17, 11am, Online

BBE Graduate Happy Hour, October 20, 5pm, Chen Breezeway

Chen Social, October 27, 5pm-7pm, Chen Breezeway/Upper Zen Garden

BBE Retreat, November 3-4, Chen Breezeway/Beckman Lawn

Dr. Matthew Meselson (Harvard) Talk, November 29, 11am-12pm, Chen 100

Winter Term Begins December 3

All upcoming events can be found on the BBE Calendar